Seonah,

> I have a strange error when I use grompp_mpi version.
> Fatal error: number of coordinates in coordinate file (trp_b4md.gro,
> 3930)
>              does not match topology (trp.top, 4677)
> When I check the .top file and .gro file, it looks ok.

Not strange at all.  Your .top says you have:

> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> SOL              1493

Just considering the water molecules that is 4479 atoms (as I have no idea how many atoms in your protein).

But in your .gro file it states that you have:

> TC5B in water
>  3930

It is only 3930.

The difference between the two numbers is equal to 249 waters, so that might be your issue, i.e. you forgot to adjust the number of waters at some time.

Catch ya,

Dallas Warren